compechem.systems sub-module#

System class#

class compechem.systems.System(filepath, charge=0, spin=1, box_side=None)#

The System object describes a generic molecular system described at a given level of theory. A system is defined based on a molecular geometry, a charge, a spin multiplicity and, one a level of theory is selected, by a set of computed properties.

Parameters:

  • filepath (str) – The path to the file containing the system geometry or data

  • charge (int, optional) – The total charge of the system. (Default: 0 neutral)

  • spin (int, optional) – The total spin multiplicity of the system. (Default: 1 singlet)

  • box_side (float, optional) – For periodic systems, defines the length (in Å) of the box side

Raises:

ValueError – Exception raised when the .xyz file path is invalid

property is_periodic: bool#

Indicates if the system is periodic or not

Returns:

True if the system is periodic (the box_side is not None), False otherwise.

Return type:

bool

save_json(path)#

Saves a JSON representation of the object that can be stored on disk and loaded (using the class constructor with the option SupportedTypes.JSON) at a later time to re-generate ad identical System object.

Parameters:

path (str) – The path to the .json file that must be created.

Return type:

None

write_gen(gen_file, box_side=None)#

Writes the current geometry to a .gen file.

Parameters:

  • gen_file (str) – path to the output .gen file

  • box_side (float, optional) – for periodic systems, defines the length (in Å) of the box side

Ensemble class#

class compechem.systems.Ensemble(systems)#

Ensemble object, containing a series of System objects.

Parameters:

systems (List[System]) – The list of System objects to be included in the Ensemble.

name#

Name of the system represented in the ensemble, taken from the first element of the ensemble

Type:

str

systems#

The list of System objects in the Ensemble.

Type:

List[System]

properties#

The property archive containing the average ensamble properties calculated at various levels of theory.

Type:

PropertiesArchive

add(systems)#

Append more Systems to the ensemble

Parameters:

systems (List[System]) – The list of systems to be added to the ensamble

property atomcount: int#

The number of atoms in the system

Returns:

The total number of atoms

Return type:

int

boltzmann_average(temperature=297.15)#

Calculates the average free Helmholtz energy of the ensemble (in Hartree), weighted for each molecule by its Boltzmann factor.

Parameters:

temperature (float) – temperature at which to calculate the Boltzmann average, by default 297.15 K

Returns:

  • float – The total Helmholtz free energy of the ensemble.

  • NOTE (the vibronic contributions are included in the electronic component, which)

  • actually contains the TOTAL energy of the system. Maybe in the future I’ll think of

  • how to separate the two contributions - LB

Return type:

float